My seqs are not from 16S gene, but from a functional genes, which were obtained clone libraries from several different environmental samples. I would like to get PCoA plot to see how different the phylogenetic relationship between samples. I would like to use Unfrac weighted distance matrix for getting PCoA plot.

I just guess that I have to obtained Unifrac weighted distance matrix from phylogenetic tree that was constructed using my sequence. Then, I may use the matrix to generate PCoA plot.